cortical_thickness
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cortical_thickness [2017/08/03 18:45] mpenrod Added longitudinal pre-processing steps |
cortical_thickness [2017/08/03 18:48] mpenrod |
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| ====Longitudinal Analysis==== | ====Longitudinal Analysis==== | ||
| + | ===Pre-processing=== | ||
| Following the segmentation of the T1-weighted image, two further pre-processing steps are necessary to proceed with longitudinal analysis of the data. Firstly, an unbiased template must be created for each subject, taking into account all time-points/sessions. Secondly, each time-point must be processed again using these templates in order to standardize subject data across time-points. | Following the segmentation of the T1-weighted image, two further pre-processing steps are necessary to proceed with longitudinal analysis of the data. Firstly, an unbiased template must be created for each subject, taking into account all time-points/sessions. Secondly, each time-point must be processed again using these templates in order to standardize subject data across time-points. | ||
| The command to create the unbiased template is: | The command to create the unbiased template is: | ||
| - | <code>recon-all -base [output file name] -tp <time-point 1 file> -tp <time-point 2 file> ... -tp <time-point n file> -all</code> | + | <code>recon-all -base [output file name] -tp [time-point 1 file] -tp [time-point 2 file] ... -tp [time-point n file] -all</code> |
| Next, the command to process each time-point using this template is: | Next, the command to process each time-point using this template is: | ||
| <code>recon-all -long [template file] [time_point file] -all</code> | <code>recon-all -long [template file] [time_point file] -all</code> | ||
| - | The **recon-all -base** command will take about as long as the original FreeSurfer segmentation, however each iteration of the **recon-all -long** command will take approximately half the time. | + | The **recon-all -base** command will take about as long as the original FreeSurfer segmentation, however each iteration of the **recon-all -long** command will take approximately half the time. Using helper functions, the **paralell_recon.m** script will also generate and execute these commands. |
| We will follow the steps outlined in the [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial|Freesurfer Wiki]] for analyzing cortical thickness. The first steps are described [[https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing|here]]. | We will follow the steps outlined in the [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial|Freesurfer Wiki]] for analyzing cortical thickness. The first steps are described [[https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing|here]]. | ||
cortical_thickness.txt · Last modified: 2017/08/04 18:58 by mpenrod
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